chemlab.db¶
AbstractDB¶
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class
chemlab.db.base.AbstractDB¶ Interface for a generic database.
A typical database can be used to retrieve molecules by calling the get method:
water = db.get("molecule", "example.water")
A database can also provide custom functionalities to store or search for entries. Those are implemented in custom methods.
See the other implementations for more relevant examples.
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get(feature, key, *args, **kwargs)¶ Get a data entry from the database.
Subclasses are required to implement this method to provide access to the database.
Parameters
- feature: str
An identifier that represents the kind of data that we want to extract. Examples of such identifier are “system”, “molecule”, “data” etc.
- key: str
The key associated with the database entry. By convention you can use dotted names to provide some kind of nested structure.
- args, kwargs:
Custom extra arguments.
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ChemlabDB¶
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class
chemlab.db.ChemlabDB¶ Chemlab default database.
This database contains some example molecules and some atomic data.
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get(self, 'molecule', key)¶ Retrieve a molecule from the database. The included molecule keys are:
- example.water
- example.norbornene
- gromacs.spc
- gromacs.spce
- gromacs.na+
- gromacs.cl-
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get(self, 'data', key) Retrieve atomic data. The available data is:
- symbols: Atomic symbols in a list.
- vdwdict: Dictionary with per-element Van Der Waals radii.
- massdict: Dictionary of masses.
- paulingenegdict: Dictionary with per-element Pauling electronegativity
- arenegdict: Dictionary with per-element Allred-Rochow electronegativity
- maxbonddict: Dictionary of maximum bond valences. 6 if unknown.
- ionpotdict: Dictionary of ionisation potentials in eV
- eaffdict: Dictionary of electron affinities in eV
Data was taken from the OpenBabel distribution.
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ChemSpiderDB¶
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class
chemlab.db.ChemSpiderDB(token=None)¶ Retrieve data from the online Chemspider database by passing an string identifier.
Parameters
- token: str | None
The chemspider security token. When token is None, chemlab will try to retrieve the token from a configuration file in $HOME/.chemlabrc that has the entry:
[chemspider] token=YOUR-SECURITY-TOKEN
The get method requires a key argument to retrieve a database entry. A valid key can be, for instance, the common name of a certain chemical, a SMILES string or an InChi identifier. This is just an adapter on the chemspipy library.
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get(self, 'inchi', key) Retrieve the InChi string for the compound.
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get(self, 'molecularformula', key) Retrieve the molecular formula as a LaTeX string.
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get(self, 'imageurl', key) Retrieve the url of a 2D image representation of the compound.
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get(self, 'smiles', key) Retrieve the SMILES string for the compound.
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get(self, 'averagemass', key) Retrieve the average mass
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get(self, 'nominalmass', key) Retrieve the nominal mass
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get(self, 'inchikey', key) Return the InChi key.
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get(self, 'alogp', key) Predicted LogP (partition coefficient) using the ACD LogP algorithm.
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get(self, 'xlogp', key) Predicted LogP using the XLogP algorithm.
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get(self, 'image', key) PNG image of the compound as a data string.
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get(self, 'mol2d', key) MOL mdl file containing 2D coordinates of the compound.
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get(self, 'commonname', key) Retrieve the common name of the compound.
LocalDB¶
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class
chemlab.db.LocalDB(directory)¶ Store serialized molecules and systems in a directory tree.
See Having your own molecular database for an example of usage.
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directory¶ Directory where the database is located.
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get(self, 'molecule', key)¶ Get an entry from the database. Key is the filename without extension of the serialized molecule. Molecules are stored in the subdirectory.
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get(self, 'system', key) Get an entry from the database. Key is the filename without extension of the serialized system.
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store(self, 'molecule', key, value)¶
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store(self, 'system', key, value) Store a Molecule or a System passed as value in the directory structure. The objects are dumped to disk after being serialized to json.
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